ChIP-Atlas: SRX7889142

Antigen

Cell type Class: Larvae
Cell type: Central Nervous System
MeSH Description: The main information-processing organs of the nervous system, consisting of the brain, spinal cord, and meninges.

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: 60 third-instar larval CNSs per biological replicate (two biological replicates per sample) were dissected in ice-cold PBS. Chromatin was prepared as described in (Gambetta, Oktaba and Müller, 2009) with the following modifications: inverted larval cuticles were cross-linked for 15 minutes at room temperature in 1.8% (v/v) paraformaldehyde, and dissected brains were sonicated in 120 µl of previously described RIPA140 buffer in AFA microtubes in a Covaris S220 sonicator (Covaris) for 5 minutes with a peak incident power of 140W, a duty cycle of 5% and 200 cycles per burst. Sonicated chromatin was centrifuged to pellet insoluble material and snap-frozen. ChIP was performed with rabbit polyclonal antibody crude sera against CTCF1-293 and Cp1901-1096 generated for this study. ChIP was performed as previously described in (Gambetta, Oktaba and Müller, 2009) except that Protein A and G Dynabeads were used. ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep kit for Illumina. An equimolar pool of multiplexed ChIP-seq libraries at 4 nM was sequenced on the Illumina HiSeq4000 (150 bp paired-end). Standard ChIP-seq libraries were prepared with the NEBNext Ultra II DNA Library Prep kit for Illumina.